The Amex not available via Apple Pay is something I've seen recently too, but the option to just enter the card number is then usually still available.

It does seem that there's been a change with payments for last-minute bookings. I played around a bit with flights departing within 3-4hrs and the Dutch website only shows iDeal as payment option. If you switch to the French or Luxembourgish website for example, you end up with an error before getting to the payment page. It'll show you a PNR and asks to call the support desk, supposedly to finish the booking by giving them the payment card data.

It's quite annoying as I often book flights last-minute for work, and having to call in every single time to get a ticket issued is just not feasible for me...